PARANA: Parsimonious Ancestral Reconstruction And Network Analysis

Overview

PARANA is an implementation of the method described in the paper Parsimonious Reconstruction of Network Evolution to perform parsimony based inference of ancestral biological networks. Given multiple extant networks and phylogenetic information relating extant nodes, PARANA finds a parsimonious set of ancestral interaction events (edge gains and losses) which explain the extant networks.
The framework adopted by PARANA is able to represent network evolution under models that support gene duplication and loss and independent interaction gain and loss. The method works on both directed and undirected networks and can incorporate asymmetric interaction gain and loss costs. In contrast to previous approaches, our method does not require knowing the relative ordering of unrelated duplication events and thus, works on phylogenetic trees even where branch lengths are not provided.

Presentation

Software

Funding

NSF

EF-0849899, IIS-0812111, CCF-1053918

NIH

1R21AI085376, R01HG002945

USDA

2008-04049, 2010-15739-01

This material is based upon work supported by the National Science
Foundation under Grant Numbers EF-0849899, IIS-0812111, CCF-1053918. Any
opinions, findings, and conclusions or recommendations expressed in this
material are those of the author(s) and do not necessarily reflect the views of
the National Science Foundation.